Re: [PyMOL] NUmber

Hi Suda,
Do you mean the number of residues in helix c.q. sheet or the number
of helices and the number of sheets? The former is pretty easy. You
can do
select ss s
select ss h
to get the numbers for sheet and helices, respectively. To use the
numbers in a script, use cmd.select('ss s') and cmd.select('ss h')
instead.
The other way is not as easy. You'll have to get the sequence:
cmd.dss()
ss = "".join([i.ss for i in cmd.get('n. ca').atom])
and then parse the sequence for stretches of identical types. In the
case of helices, that will give you the answer, but sheets are
typically composed of multiple strands, which will require additional
effort.
Hope it helps,
Tsjerk
On Wed, Sep 21, 2011 at 5:47 AM, Suda Ravindran <biobudhan@...> wrote:
> Hi,
>
> I would like to know if there is any option in PyMol to count the number of
> helices and sheets present in the structure.????
>
> Please help me out..
>
> -Suda
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...
>
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

Hi Suda,
Do you mean the number of residues in helix c.q. sheet or the number
of helices and the number of sheets? The former is pretty easy. You
can do
select ss s
select ss h
to get the numbers for sheet and helices, respectively. To use the
numbers in a script, use cmd.select('ss s') and cmd.select('ss h')
instead.
The other way is not as easy. You'll have to get the sequence:
cmd.dss()
ss = "".join([i.ss for i in cmd.get('n. ca').atom])
and then parse the sequence for stretches of identical types. In the
case of helices, that will give you the answer, but sheets are
typically composed of multiple strands, which will require additional
effort.
Hope it helps,
Tsjerk
On Wed, Sep 21, 2011 at 5:47 AM, Suda Ravindran <biobudhan@...> wrote:
> Hi,
>
> I would like to know if there is any option in PyMol to count the number of
> helices and sheets present in the structure.????
>
> Please help me out..
>
> -Suda
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...
>
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands